151
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Ly L, Wasinger VC. Peptide enrichment and protein fractionation using selective electrophoresis. Proteomics 2009; 8:4197-208. [PMID: 18814323 DOI: 10.1002/pmic.200701088] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In recent times, the analysis of the peptidome has become increasingly valuable to gain a better understanding of the critical roles native peptides play in biological processes. Here, we show a technique using a novel electrophoretic device named MF10, for the fractionation of proteins and peptides based on size and also pH in low volume liquid phase under an electric field. A 1 microM, 7-protein and peptide standard mix ranging from 1 to 25 kDa has been used to show peptide migration into a fraction contained by 1-5 kDa membranes. Simultaneous fractionation of the higher mass protein standards to the correct fraction also occurred. To assess the MF10's ability to fractionate more complex samples, human plasma was used to enrich for the peptidome below 5 kDa in the presence of the proteome. Peptide enrichment was achieved while simultaneously fractionating higher mass proteins to three other mass restricted fractions. The utility of this approach is demonstrated with the identification (with at least 2 ppm mass accuracy) of 76 unique peptides, equating to 22 proteins enriched to the 1-5 kDa fraction of the MF10.
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Affiliation(s)
- Linda Ly
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, Australia
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152
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Abstract
The human central nervous system (CNS) is the most complex organ in nature, composed of ten trillion cells forming complex neural networks using a quadrillion synaptic connections. Proteins, their modifications, and their interactions are integral to CNS function. The emerging field of neuroproteomics provides us with a wide-scope view of posttranslation protein dynamics within the CNS to better our understanding of its function, and more often, its dysfunction consequent to neurodegenerative disorders. This chapter reviews methodology employed in the neurosciences to study the neuroproteome in health and disease. The chapter layout parallels this volume's four parts. Part I focuses on modeling human neuropathology in animals as surrogate, accessible, and controllable platforms in our research. Part II discusses methodology used to focus analysis onto a subneuroproteome. Part III reviews analytical and bioinformatic technologies applied in neuroproteomics. Part IV discusses clinical neuroproteomics, from processing of human biofluids to translation in biomarkers research. Neuroproteomics continues to mature as a discipline, confronting the extreme complexity of the CNS proteome and its dynamics, and providing insight into the molecular mechanisms underlying how our nervous system works and how it is compromised by injury and disease.
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153
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Abstract
The degree of protein diversity and dynamic range within organisms means that even the simplest proteome cannot be captured by any single extraction and separation step. New techniques have focused on major protein classes often under-represented in proteome analysis; low abundance, membrane, and alkaline proteins. The last decade has seen considerable technology development in fractionation tools aimed at complexity reduction in many forms. The key outcome of complexity reduction is that each fraction, or sub-proteome, can be studied in more detail, and proteins which would have remained undetected in a total extract are present in sufficient quantities. However, the tools available are fractionations, not amplifications, and like all mining for rare and difficult items, a large amount of starting material is often required. The key shortcomings of many proteome analysis techniques are now well documented. With this knowledge, the best modern proteomics 'platform' involves combining multiple protein extractions, gel and chromatographic separations, and multiple MS analysis methods.
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Affiliation(s)
- Ben Herbert
- Department of Medical and Molecular Biosciences, University of Technology, Sydney, 15 Broadway, Ultimo, Sydney, NSW 2007, Australia
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154
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Jmeian Y, El Rassi Z. Liquid-phase-based separation systems for depletion, prefractionation and enrichment of proteins in biological fluids for in-depth proteomics analysis. Electrophoresis 2009; 30:249-61. [DOI: 10.1002/elps.200800639] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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155
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Farinazzo A, Restuccia U, Bachi A, Guerrier L, Fortis F, Boschetti E, Fasoli E, Citterio A, Righetti PG. Chicken egg yolk cytoplasmic proteome, mined via combinatorial peptide ligand libraries. J Chromatogr A 2008; 1216:1241-52. [PMID: 19081572 DOI: 10.1016/j.chroma.2008.11.051] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Revised: 11/16/2008] [Accepted: 11/18/2008] [Indexed: 11/28/2022]
Abstract
The use of combinatorial peptide ligand libraries (CPLLs), containing hexapeptides terminating with a primary amine, or modified with a terminal carboxyl group, or with a terminal tertiary amine, allowed discovering and identifying a large number of previously unreported egg yolk proteins. Whereas the most comprehensive list up to date [K. Mann, M. Mann, Proteomics, 8 (2008) 178-191] tabulated about 115 unique gene products in the yolk plasma, our findings have more than doubled this value to 255 unique protein species. From the initial non-treated egg yolk it was possible to find 49 protein species; the difference was generated thanks to the use of the three combined CPLLs. The aberrant behaviour of some proteins, upon treatment via the CPLL method, such as proteins that do not interact with the library, is discussed and evaluated. Simplified elution protocols from the CPLL beads are taken into consideration, of which direct elution in a single step via sodium dodecyl sulphate desorption seems to be quite promising. Alternative methods are suggested. The list of egg yolk components here reported is by far the most comprehensive at present and could serve as a starting point for isolation and functional characterization of proteins possibly having novel pharmaceutical and biomedical applications.
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Affiliation(s)
- Alessia Farinazzo
- Department of Chemistry, Materials and Chemical Egineering Giulio Natta, Politecnico di Milano, Via Mancinelli 7, 20131 Milan, Italy
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156
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Righetti PG, Boschetti E. The ProteoMiner and the FortyNiners: searching for gold nuggets in the proteomic arena. MASS SPECTROMETRY REVIEWS 2008; 27:596-608. [PMID: 18481254 DOI: 10.1002/mas.20178] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The present review covers modern aspects of combinatorial peptide ligand libraries (CPLL), as used to analyze the "low-abundance proteome" in association with mass spectrometry. First, the capturing properties of baits of different lengths (from single amino acid to hexa-peptides) are described to show that a plateau is rapidly reached above a tetra-peptide in length, thus confirming the validity of having adopted hexapeptides for the considered application. The mechanism of interaction with proteins from very complex proteomes and the ability to decrease the dynamic concentration range is demonstrated with the help of mass spectrometry analysis. Examples are given on how treatment with CPLLs dramatically improves the detectability of peptides in mass spectrometry analysis, permitting detection of a very large number of proteins as compared with control, untreated samples. The use of complementary libraries is discussed with the aim to discover additional low-abundance species that escaped the first library. A discussion on the possibility to discover extremely rare gene products, and the quantitative aspect of the technology when associated with mass spectrometry is also provided. Some insights on the applications for hidden, low-abundance biomarkers are also presented.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering Giulio Natta, Polytechnic of Milano, 20131 Milan, Italy.
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157
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Sihlbom C, Kanmert I, Bahr HV, Davidsson P. Evaluation of the combination of bead technology with SELDI-TOF-MS and 2-D DIGE for detection of plasma proteins. J Proteome Res 2008; 7:4191-8. [PMID: 18690747 DOI: 10.1021/pr800340c] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Today biomarker discovery is one of the most active aspects of proteomic investigations. However, the wide dynamic range of plasma proteins makes the analysis very challenging because high abundance proteins tend to mask those of lower abundance. Using a large bead-based library of combinatorial peptide ligands (Equalizer beads or ProteoMiner), the dynamic range of the protein concentration is compressed, the high abundance proteins present in the sample are reduced and the low abundance proteins are enriched, while retaining representatives of all proteins within the sample. In the present study, the combination of beads with surface enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS) and two-dimensional differential gel electrophoresis (2-D DIGE) technology were evaluated considering efficiency, reproducibility, sensitivity, and compatibility. The bead technology is easily compatible with both SELDI-TOF-MS and 2-D DIGE and the samples can be analyzed directly without any processing of the sample. The use of the beads prior SELDI-TOF-MS and 2-D DIGE enabled detection of many new protein spots/peaks and increased resolution and improved intensity of low abundance proteins in a reproducible fashion compared with the depletion technique. Several proteins have been identified by the combination of beads, 2-D DIGE and MS for example different kinds of complement factors and cytoskeletal proteins. Our data suggest that integration of the bead technology with our current proteomic technologies will enhance the possibility to deliver new peptide/protein biomarker candidates in our projects.
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158
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Flow field-flow fractionation: A pre-analytical method for proteomics. J Proteomics 2008; 71:265-76. [DOI: 10.1016/j.jprot.2008.06.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Revised: 06/02/2008] [Accepted: 06/05/2008] [Indexed: 02/05/2023]
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159
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Boschetti E, Righetti PG. The ProteoMiner in the proteomic arena: A non-depleting tool for discovering low-abundance species. J Proteomics 2008; 71:255-64. [DOI: 10.1016/j.jprot.2008.05.002] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 05/20/2008] [Accepted: 05/22/2008] [Indexed: 10/22/2022]
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160
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Roux-Dalvai F, Gonzalez de Peredo A, Simó C, Guerrier L, Bouyssié D, Zanella A, Citterio A, Burlet-Schiltz O, Boschetti E, Righetti PG, Monsarrat B. Extensive analysis of the cytoplasmic proteome of human erythrocytes using the peptide ligand library technology and advanced mass spectrometry. Mol Cell Proteomics 2008; 7:2254-69. [PMID: 18614565 DOI: 10.1074/mcp.m800037-mcp200] [Citation(s) in RCA: 200] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The erythrocyte cytoplasmic proteome is composed of 98% hemoglobin; the remaining 2% is largely unexplored. Here we used a combinatorial library of hexameric peptides as a capturing agent to lower the signal of hemoglobin and amplify the signal of low to very low abundance proteins in the cytoplasm of human red blood cells (RBCs). Two types of hexapeptide library beads have been adopted: amino-terminal hexapeptide beads and beads in which the peptides have been further derivatized by carboxylation. The amplification of the signal of low abundance and suppression of the signal of high abundance species were fully demonstrated by two-dimensional gel maps and nano-LC-MSMS analysis. The effect of this new methodology on quantitative information also was explored. Moreover using this approach on an LTQ-Orbitrap mass spectrometer, we could identify with high confidence as many as 1578 proteins in the cytoplasmic fraction of a highly purified preparation of RBCs, allowing a deep exploration of the classical RBC pathways as well as the identification of unexpected minor proteins. In addition, we were able to detect the presence of eight different hemoglobin chains including embryonic and newly discovered globin chains. Thus, this extensive study provides a huge data set of proteins that are present in the RBC cytoplasm that may help to better understand the biology of this simplified cell and may open the way to further studies on blood pathologies using targeted approaches.
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Affiliation(s)
- Florence Roux-Dalvai
- Institute of Pharmacology and Structural Biology, CNRS, Université de Toulouse, 31077 Toulouse, France
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161
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Fang X, Zhang WW. Affinity separation and enrichment methods in proteomic analysis. J Proteomics 2008; 71:284-303. [PMID: 18619565 DOI: 10.1016/j.jprot.2008.06.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Revised: 06/24/2008] [Accepted: 06/24/2008] [Indexed: 12/24/2022]
Abstract
Protein separation or enrichment is one of the rate-limiting steps in proteomic studies. Specific capture and removal of highly-abundant proteins (HAP) with large sample-handling capacities are in great demand for enabling detection and analysis of low-abundant proteins (LAP). How to grasp and enrich these specific proteins or LAP in complex protein mixtures is also an outstanding challenge for biomarker discovery and validation. In response to these needs, various approaches for removal of HAP or capture of LAP in biological fluids, particularly in plasma or serum, have been developed. Among them, immunoaffinity subtraction methods based upon polyclonal IgY or IgG antibodies have shown to possess unique advantages for proteomic analysis of plasma, serum and other biological samples. In addition, other affinity methods that use recombinant proteins, lectins, peptides, or chemical ligands have also been developed and applied to LAP capture or enrichment. This review discusses in detail the need to put technologies and methods in affinity subtraction or enrichment into a context of proteomic and systems biology as "Separomics" and provides a prospective of affinity-mediated proteomics. Specific products, along with their features, advantages, and disadvantages will also be discussed.
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162
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Martins de Souza D, Oliveira BM, Castro-Dias E, Winck FV, Horiuchi RSO, Baldasso PA, Caetano HT, Pires NKD, Marangoni S, Novello JC. The untiring search for the most complete proteome representation: reviewing the methods. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 7:312-21. [DOI: 10.1093/bfgp/eln023] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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163
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D’Ambrosio C, Arena S, Scaloni A, Guerrier L, Boschetti E, Mendieta ME, Citterio A, Righetti PG. Exploring the Chicken Egg White Proteome with Combinatorial Peptide Ligand Libraries. J Proteome Res 2008; 7:3461-74. [DOI: 10.1021/pr800193y] [Citation(s) in RCA: 135] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Chiara D’Ambrosio
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147, Naples, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milan, Italy
| | - Simona Arena
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147, Naples, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milan, Italy
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147, Naples, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milan, Italy
| | - Luc Guerrier
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147, Naples, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milan, Italy
| | - Egisto Boschetti
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147, Naples, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milan, Italy
| | - Martha Elena Mendieta
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147, Naples, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milan, Italy
| | - Attilio Citterio
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147, Naples, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milan, Italy
| | - Pier Giorgio Righetti
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147, Naples, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milan, Italy
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164
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Cappadona S, Levander F, Jansson M, James P, Cerutti S, Pattini L. Wavelet-based method for noise characterization and rejection in high-performance liquid chromatography coupled to mass spectrometry. Anal Chem 2008; 80:4960-8. [PMID: 18510348 DOI: 10.1021/ac800166w] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a new method for rejecting noise from HPLC-MS data sets. The algorithm reveals peptides at low concentrations by minimizing both the chemical and the random noise. The goal is reached through a systematic approach to characterize and remove the background. The data are represented as two-dimensional maps, in order to optimally exploit the complementary dimensions of separation of the peptides offered by the LC-MS technique. The virtual chromatograms, reconstructed from the spectrographic data, have proved to be more suitable to characterize the noise than the raw mass spectra. By means of wavelet analysis, it was possible to access both the chemical and the random noise, at different scales of the decomposition. The novel approach has proved to efficiently distinguish signal from noise and to selectively reject the background while preserving low-abundance peptides.
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Affiliation(s)
- Salvatore Cappadona
- Department of Bioengineering, IIT Unit, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
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165
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Bertucci F, Goncalves A. Clinical proteomics and breast cancer: strategies for diagnostic and therapeutic biomarker discovery. Future Oncol 2008; 4:271-87. [PMID: 18407739 DOI: 10.2217/14796694.4.2.271] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A major challenge of breast cancer research is the identification of accurate biomarkers that improve screening, early diagnosis, prediction of aggressiveness, and prediction of therapeutic response or toxicity, as well as the identification of new molecular therapeutic targets. The new proteomic techniques promise to be valuable for identifying such tissue and serum markers. The different techniques currently applied to clinical samples of breast cancer and the most important results obtained are summarized in this review.
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Affiliation(s)
- François Bertucci
- Institut Paoli-Calmettes and UMR599, Centre de Recherche en Cancérologie de Marseille, Département d'Oncologie Moléculaire, 232, Bd Sainte-Marguerite 13009 Marseille, France.
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166
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Guerrier L, Righetti PG, Boschetti E. Reduction of dynamic protein concentration range of biological extracts for the discovery of low-abundance proteins by means of hexapeptide ligand library. Nat Protoc 2008; 3:883-90. [DOI: 10.1038/nprot.2008.59] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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167
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Bachi A, Simó C, Restuccia U, Guerrier L, Fortis F, Boschetti E, Masseroli M, Righetti PG. Performance of Combinatorial Peptide Libraries in Capturing the Low-Abundance Proteome of Red Blood Cells. 2. Behavior of Resins Containing Individual Amino Acids. Anal Chem 2008; 80:3557-65. [DOI: 10.1021/ac8001353] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Angela Bachi
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Department of Electronics and Informatics, Polytechnic of Milano, 20133 Milano, Italy
| | - Carolina Simó
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Department of Electronics and Informatics, Polytechnic of Milano, 20133 Milano, Italy
| | - Umberto Restuccia
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Department of Electronics and Informatics, Polytechnic of Milano, 20133 Milano, Italy
| | - Luc Guerrier
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Department of Electronics and Informatics, Polytechnic of Milano, 20133 Milano, Italy
| | - Frederic Fortis
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Department of Electronics and Informatics, Polytechnic of Milano, 20133 Milano, Italy
| | - Egisto Boschetti
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Department of Electronics and Informatics, Polytechnic of Milano, 20133 Milano, Italy
| | - Marco Masseroli
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Department of Electronics and Informatics, Polytechnic of Milano, 20133 Milano, Italy
| | - Pier Giorgio Righetti
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Department of Electronics and Informatics, Polytechnic of Milano, 20133 Milano, Italy
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168
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Simó C, Bachi A, Cattaneo A, Guerrier L, Fortis F, Boschetti E, Podtelejnikov A, Righetti PG. Performance of Combinatorial Peptide Libraries in Capturing the Low-Abundance Proteome of Red Blood Cells. 1. Behavior of Mono- to Hexapeptides. Anal Chem 2008; 80:3547-56. [DOI: 10.1021/ac702635v] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carolina Simó
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, San Raffaele Scientific Institute, 20132 Milano, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Proxeon A/S, DK-5230 Odense, Denmark
| | - Angela Bachi
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, San Raffaele Scientific Institute, 20132 Milano, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Proxeon A/S, DK-5230 Odense, Denmark
| | - Angela Cattaneo
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, San Raffaele Scientific Institute, 20132 Milano, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Proxeon A/S, DK-5230 Odense, Denmark
| | - Luc Guerrier
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, San Raffaele Scientific Institute, 20132 Milano, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Proxeon A/S, DK-5230 Odense, Denmark
| | - Frederic Fortis
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, San Raffaele Scientific Institute, 20132 Milano, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Proxeon A/S, DK-5230 Odense, Denmark
| | - Egisto Boschetti
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, San Raffaele Scientific Institute, 20132 Milano, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Proxeon A/S, DK-5230 Odense, Denmark
| | - Alexander Podtelejnikov
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, San Raffaele Scientific Institute, 20132 Milano, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Proxeon A/S, DK-5230 Odense, Denmark
| | - Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, San Raffaele Scientific Institute, 20132 Milano, Italy, Bio-Rad Laboratories, C/o CEA-Saclay 91181 Gif-sur-Yvette, France, and Proxeon A/S, DK-5230 Odense, Denmark
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169
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Kussmann M, Rezzi S, Daniel H. Profiling techniques in nutrition and health research. Curr Opin Biotechnol 2008; 19:83-99. [DOI: 10.1016/j.copbio.2008.02.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Revised: 02/13/2008] [Accepted: 02/14/2008] [Indexed: 12/13/2022]
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170
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Hexapeptide combinatorial ligand libraries: the march for the detection of the low-abundance proteome continues. Biotechniques 2008; 44:663-5. [DOI: 10.2144/000112762] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
After 10 years of extensive proteomic research, it has become increasingly apparent that new technologies are sorely needed for detecting the low-abundance proteome—those proteins (up to 50% in any proteome) whose concentration in tissues or cells falls below the detection limits of currently available methodologies. Here we survey one such method: a combinatorial ligand library (called ProteoMiner), comprising dozens of millions of hexapeptides capable of interacting with most, if not all, proteins in any given proteome. They act by drastically reducing the signal of high-abundance species while increasing the level of the low-abundance components to bring their signal within the detection limit of present-day tools. Such a library has been tested against a number of human biological fluids, such as sera, urine, cerebrospinal fluid as well as against cell lysates (e.g., platelets, red blood cells) with interesting results.
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171
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Experimental and computational approaches to quantitative proteomics: Status quo and outlook. J Proteomics 2008; 71:19-33. [DOI: 10.1016/j.jprot.2007.12.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 12/14/2007] [Accepted: 12/18/2007] [Indexed: 01/11/2023]
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172
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Cieniewski-Bernard C, Acosta A, Dubois E, Lamblin N, Beseme O, Chwastyniak M, Amouyel P, Bauters C, Pinet F. PROTEOMIC ANALYSIS IN CARDIOVASCULAR DISEASES. Clin Exp Pharmacol Physiol 2008; 35:362-6. [DOI: 10.1111/j.1440-1681.2008.04878.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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173
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Liumbruno G, D'Amici GM, Grazzini G, Zolla L. Transfusion medicine in the era of proteomics. J Proteomics 2008; 71:34-45. [DOI: 10.1016/j.jprot.2008.02.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Revised: 02/18/2008] [Accepted: 02/18/2008] [Indexed: 12/21/2022]
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174
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Shores KS, Udugamasooriya DG, Kodadek T, Knapp DR. Use of peptide analogue diversity library beads for increased depth of proteomic analysis: application to cerebrospinal fluid. J Proteome Res 2008; 7:1922-31. [PMID: 18357977 DOI: 10.1021/pr7006889] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Biological samples can contain proteins with concentrations that span more than 10 orders of magnitude. Given the limited dynamic range of analysis methods, observation of proteins present at the lower concentrations requires depletion of high-abundance proteins, or other means of reducing the dynamic range of concentrations. Hexapeptide diversity library beads have been used to bind proteins in a complex sample up to a given saturation limit, effectively truncating the maximum concentration of proteins at a desired level. To avoid the potential problem of susceptibility of the hexapeptides to cleavage by proteases in the sample and/or bacterial degradation, peptide analogues that exhibit similar binding characteristics to peptides can be used in place of peptides. We report here the use of hexameric peptoid diversity library beads to reduce the dynamic range of protein concentrations in human cerebrospinal fluid (CSF). Using this method in conjunction with 2D LC/MS/MS analyses, we identified 200 unique proteins, about twice the number identified in untreated CSF.
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Affiliation(s)
- Kevin S Shores
- Department of Pharmacology and MUSC Proteomics Center, Medical University of South Carolina, Charleston, SC 29425, USA
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175
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Abstract
This 2006 'Plant Proteomics Update' is a continuation of the two previously published in 'Proteomics' by 2004 (Canovas et al., Proteomics 2004, 4, 285-298) and 2006 (Rossignol et al., Proteomics 2006, 6, 5529-5548) and it aims to bring up-to-date the contribution of proteomics to plant biology on the basis of the original research papers published throughout 2006, with references to those appearing last year. According to the published papers and topics addressed, we can conclude that, as observed for the three previous years, there has been a quantitative, but not qualitative leap in plant proteomics. The full potential of proteomics is far from being exploited in plant biology research, especially if compared to other organisms, mainly yeast and humans, and a number of challenges, mainly technological, remain to be tackled. The original papers published last year numbered nearly 100 and deal with the proteome of at least 26 plant species, with a high percentage for Arabidopsis thaliana (28) and rice (11). Scientific objectives ranged from proteomic analysis of organs/tissues/cell suspensions (57) or subcellular fractions (29), to the study of plant development (12), the effect of hormones and signalling molecules (8) and response to symbionts (4) and stresses (27). A small number of contributions have covered PTMs (8) and protein interactions (4). 2-DE (specifically IEF-SDS-PAGE) coupled to MS still constitutes the almost unique platform utilized in plant proteome analysis. The application of gel-free protein separation methods and 'second generation' proteomic techniques such as multidimensional protein identification technology (MudPIT), and those for quantitative proteomics including DIGE, isotope-coded affinity tags (ICAT), iTRAQ and stable isotope labelling by amino acids in cell culture (SILAC) still remains anecdotal. This review is divided into seven sections: Introduction, Methodology, Subcellular proteomes, Development, Responses to biotic and abiotic stresses, PTMs and Protein interactions. Section 8 summarizes the major pitfalls and challenges of plant proteomics.
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Affiliation(s)
- Jesús V Jorrín
- Agricultural and Plant Biochemistry Research Group-Plant Proteomics, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain.
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176
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Guerrier L, Claverol S, Finzi L, Paye F, Fortis F, Boschetti E, Housset C. Contribution of solid-phase hexapeptide ligand libraries to the repertoire of human bile proteins. J Chromatogr A 2007; 1176:192-205. [PMID: 18036598 DOI: 10.1016/j.chroma.2007.11.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 11/02/2007] [Accepted: 11/05/2007] [Indexed: 12/26/2022]
Abstract
Proteins in bile may have important physiological functions and serve as disease biomarkers. Here, the protein composition of human gallbladder bile was analyzed using a recently described chromatography-like technology capable to enhance the signal of low-abundance species. First, proteins present in bile fluid were treated with immobilized peptide ligand libraries to concentrate dilute and very dilute species while concomitantly diluting the high-abundance proteins. The analysis of resulting protein mixture was then performed using LC-MS/MS after having classically separated proteins by a mini preparative gel electrophoresis. Overall 222 gene products were found; 143 of them were not reported before in proteomics studies. Ligand libraries by themselves contributed to find 81 new gene products distributed throughout different categories. The described chromatographic approach provides a significant contribution to the bile protein repertoire and opens new perspectives for the discovery of markers for specific biliary tract diseases.
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Affiliation(s)
- L Guerrier
- Bio-Rad Laboratories, C/o CEA-Saclay, Gif-sur-Yvette, France
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177
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Shores KS, Knapp DR. Assessment Approach for Evaluating High Abundance Protein Depletion Methods for Cerebrospinal Fluid (CSF) Proteomic Analysis. J Proteome Res 2007; 6:3739-51. [PMID: 17696521 DOI: 10.1021/pr070293w] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Optimal proteomic analysis of human cerebrospinal fluid (CSF) requires depletion of high-abundance proteins to facilitate observation of low-abundance proteins. The performance of two immunodepletion (MARS, Agilent Technologies and ProteoSeek, Pierce Biotechnology) and one ultrafiltration (50 kDa molecular weight cutoff filter, Millipore Corporation) methods for depletion of abundant CSF proteins were compared using a graphical method to access the depth of analysis using "marker proteins" with known normal concentration ranges. Two-dimensional LC/MS/MS analysis of each depleted sample yielded 171 and 163 unique protein identifications using the MARS and ProteoSeek immunodepletion methods, respectively, while only 46 unique proteins were identified using a 50 kDa molecular weight cutoff filter. The relative abundance of the identified proteins was estimated using total spectrum counting and compared to the concentrations of 45 known proteins in CSF as markers of the analysis depth. Results of this work suggest a clear need for methodology designed specifically for depletion of high-abundance proteins in CSF, as depletion methods designed to deplete high-abundance serum proteins showed little improvement in analysis depth compared to analysis without depletion. The marker protein method should be generally useful for assessing depth of analysis in the comparison of proteomic analysis methods.
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Affiliation(s)
- Kevin S Shores
- Department of Pharmacology and MUSC Proteomics Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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178
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Doherty MK, McLean L, Beynon RJ. Avian proteomics: advances, challenges and new technologies. Cytogenet Genome Res 2007; 117:358-69. [PMID: 17675879 DOI: 10.1159/000103199] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 11/30/2006] [Indexed: 11/19/2022] Open
Abstract
Proteomics is defined as an analysis of the full complement of proteins of a cell or tissue under given conditions. Avian proteomics, or more specifically chicken proteomics, has focussed on the study of individual tissues and organs of interest to specific researchers. Researchers have looked at skeletal muscle and growth, and embryonic development and have performed initial studies in avian disease. Traditional proteomics involves identifying and cataloguing proteins in a cell and identifying relative changes in populations between two or more states, be that physiological or disease-induced states. Recent advances in proteomic technologies have included absolute quantification, proteome simplification and the ability to determine the turnover of individual proteins in a global context. This review discusses the current developments in this relatively new field, new technologies and how they may be applied to biological questions, and the challenges faced by researchers in this ever-expanding and exciting field.
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Affiliation(s)
- M K Doherty
- Protein Function Group, Department of Veterinary Preclinical Sciences, University of Liverpool, Liverpool, UK
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179
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Shave E, Vigh G. Use of a preparative-scale, recirculating isoelectric trapping device for the isolation and enrichment of acidic proteins in bovine serum. J Chromatogr A 2007; 1155:237-41. [PMID: 17383662 DOI: 10.1016/j.chroma.2007.01.125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Revised: 01/09/2007] [Accepted: 01/19/2007] [Indexed: 10/23/2022]
Abstract
A recirculating, preparative-scale isoelectric trapping device, developed for the binary isoelectric trapping separation of proteins has been used to desalt, isolate and enrich the pI<4 protein fraction from a 150 mL sample of bovine serum. Subsequent re-separation of the 2<pI<4 fraction with pH 3.0, 3.5 and 3.9 buffering membranes resulted in distinct, narrow pI fractions whose components could be readily analyzed by reversed-phase HPLC, even though they were below the detection limit in the original bovine serum sample. The entire isoelectric trapping process (from desalting to collection of the final, narrow pI fractions) took only 7h, indicating the potential of the recirculating, preparative-scale isoelectric trapping device as a front-end component in the proteomic work-flow when sufficiently large samples are available.
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Affiliation(s)
- Evan Shave
- Department of Chemistry, Texas A&M University, College Station, TX 77842-3012, USA
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180
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Cañas B, Piñeiro C, Calvo E, López-Ferrer D, Gallardo JM. Trends in sample preparation for classical and second generation proteomics. J Chromatogr A 2007; 1153:235-58. [PMID: 17276441 DOI: 10.1016/j.chroma.2007.01.045] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 12/18/2006] [Accepted: 01/12/2007] [Indexed: 11/16/2022]
Abstract
Sample preparation is a fundamental step in the proteomics workflow. However, it is not easy to find compiled information updating this subject. In this paper, the strategies and protocols for protein extraction and identification, following either classical or second generation proteomics methodologies, are reviewed. Procedures for: tissue disruption, cell lysis, sample pre-fractionation, protein separation by 2-DE, protein digestion, mass spectrometry analysis, multidimensional peptide separations and quantification of protein expression level are described.
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Affiliation(s)
- Benito Cañas
- Dept. Química Analítica, Facultad de CC, Químicas, UCM, Av.Complutense s/n, Madrid 28040, Spain.
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181
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Boschetti E, Lomas L, Citterio A, Righetti PG. Romancing the “hidden proteome”, Anno Domini two zero zero seven. J Chromatogr A 2007; 1153:277-90. [PMID: 17321532 DOI: 10.1016/j.chroma.2007.01.136] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Revised: 01/14/2007] [Accepted: 01/19/2007] [Indexed: 11/28/2022]
Abstract
The mechanism of action and properties of a solid-phase ligand library made of hexapeptides, for capturing the "hidden proteome", i.e. the low- and very low-abundance proteins constituting the vast majority of species in any proteome, be it a cell or tissue lysate or a biological fluid, are here reviewed. Mechanisms of adsorption are evaluated, as well as different protocols for en bloc or sequential elution of the captured polypeptides. Examples are given of capture of proteins from serum, human platelet extracts, bacterial extract and egg white. The increment in detection of low-abundance species appears to be of at least four-fold as compared with untreated samples. One particular aspect of this capture is the adsorption of a high proportion of small peptides (in the Mr 600-8000 Da range) that are normally lost upon electrophoretic two-dimensional mapping. Such a peptide population, in human sera, may be of particular importance since it may contain protein cleavage products of diagnostic value.
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182
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Antonioli P, Fortis F, Guerrier L, Rinalducci S, Zolla L, Righetti PG, Boschetti E. Capturing and amplifying impurities from purified recombinant monoclonal antibodiesvia peptide library beads: A proteomic study. Proteomics 2007; 7:1624-33. [PMID: 17436265 DOI: 10.1002/pmic.200600778] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Capture and amplification of low-level contaminants in purified preparations of recombinant DNA products is described here in the case of mAb meant for human consumption. Such a process is based on treatment with a vastly heterogeneous ligand library composed of hexapeptides bound to a polyhydroxymethacrylate resin. Upon this treatment, a protein solution is recovered with "normalized" relative concentration ratios, in which high-abundance proteins are strongly reduced and rare proteins are highly concentrated. Upon 2-D map analysis, the relatively few spots present in control monoclonals were seen to increase in number, reaching >100 visible polypeptide chains in the pI/M(r) plane. Most of these newly emerged spots were subjected to MS analysis and were found to be composed mainly of three classes of proteins: those derived from proteins present in the culture broth (notably albumin and transferrin), fragments of the desired final product, covering M(r) ranges from as low as 5 up to 45 kDa and some aggregates of light and heavy chains of Igs (mostly dimers and trimers). This ligand library thus appears to be a formidable tool for exploring and bringing to the limelight the "hidden proteome".
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Affiliation(s)
- Paolo Antonioli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, Milano, Italy
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183
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Norden AGW, Rodriguez-Cutillas P, Unwin RJ. Clinical urinary peptidomics: learning to walk before we can run. Clin Chem 2007; 53:375-6. [PMID: 17327502 DOI: 10.1373/clinchem.2006.084038] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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184
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Abstract
Synaptic vesicles are key organelles in neurotransmission. Vesicle integral or membrane-associated proteins mediate the various functions the organelle fulfills during its life cycle. These include organelle transport, interaction with the nerve terminal cytoskeleton, uptake and storage of low molecular weight constituents, and the regulated interaction with the pre-synaptic plasma membrane during exo- and endocytosis. Within the past two decades, converging work from several laboratories resulted in the molecular and functional characterization of the proteinaceous inventory of the synaptic vesicle compartment. However, up until recently and due to technical difficulties, it was impossible to screen the entire organelle thoroughly. Recent advances in membrane protein identification and mass spectrometry (MS) have dramatically promoted this field. A comparison of different techniques for elucidating the proteinaceous composition of synaptic vesicles revealed numerous overlaps but also remarkable differences in the protein constituents of the synaptic vesicle compartment, indicating that several protein separation techniques in combination with differing MS approaches are required to identify and characterize the synaptic vesicle proteome. This review highlights the power of various gel separation techniques and MS analyses for the characterization of the proteome of highly purified synaptic vesicles. Furthermore, the newly detected protein assignments to synaptic vesicles, especially those proteins which are new to the inventory of the synaptic vesicle proteome, are critically discussed.
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Affiliation(s)
- Jacqueline Burré
- Institute of Cell Biology and Neuroscience, Neurochemistry, JW Goethe University, Frankfurt, Germany.
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185
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Poon TCW. Opportunities and limitations of SELDI-TOF-MS in biomedical research: practical advices. Expert Rev Proteomics 2007; 4:51-65. [PMID: 17288515 DOI: 10.1586/14789450.4.1.51] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry, or surface-enhanced laser desorption/ionization ProteinChip technology, has been widely used in obtaining the quantitative profiles of tissue proteomes, particularly plasma proteomes. Its high-throughput nature and simplicity in its experimental procedures have allowed this technology to become a popular research tool for biomarker discovery in the past 5 years. After accumulating more research experiences, researchers now have a better understanding of the characteristics and limitations of this technology, as well as the pitfalls in biomarker research, by undertaking a comparative proteomic approach. This review provides an overview of the surface-enhanced laser desorption/ionization time-of-flight mass spectrometry, discusses its limitations and provides some possible solutions to help apply this technology to biomarker research.
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Affiliation(s)
- Terence C W Poon
- Li Ka Shing Institute of Health Sciences, Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region, China.
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186
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Hodgetts A, Levin M, Kroll JS, Langford PR. Biomarker discovery in infectious diseases using SELDI. Future Microbiol 2007; 2:35-49. [PMID: 17661674 DOI: 10.2217/17460913.2.1.35] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Surface enhanced laser desorption ionization–time of flight is a mass spectrometric-based method that requires a minimal amount of sample for analysis and can be used for high-throughput screening. It has been used to discover serum or tissue protein signatures and biomarkers for infectious diseases in the fields of virology (hepatitis B and C viruses, severe acute respiratory syndrome, HIV-1, human T-cell leukemia virus-1 and BK virus), parasitology (trypanosomiasis) and bacteriology (intra-amniotic inflammation, tuberculosis and bacterial endocarditis). The protein signatures, or biomarkers, can be used to diagnose infection, predict disease states and to inform on disease processes. Careful attention to experimental design, sample handling and storage, and the use of appropriate internal controls is crucial to success.
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Affiliation(s)
- Andrea Hodgetts
- Imperial College London, Department of Paediatrics, Division of Medicine, St Mary's Campus, London, UK.
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187
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Abstract
The performance of a hexapeptide ligand library in capturing the 'hidden proteome' is illustrated and evaluated. This library, insolubilized on an organic polymer and available under the trade name 'Equalizer Bead Technology', acts by capturing all components of a given proteome, by concentrating rare and very rare proteins, and simultaneously diluting the abundant ones. This results in a proteome of 'normalized' relative abundances, amenable to analysis by MS and any other analytical tool. Examples are given of analysis of human urine and serum, as well as cell and tissue lysates, such as Escherichia coli and Saccharomyces cerevisiae extracts. Another important application is impurity tracking and polishing of recombinant DNA products, especially biopharmaceuticals meant for human consumption.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering Giulio Natta, Polytechnic of Milano, Milan, Italy.
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188
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Vercauteren FGG, Arckens L, Quirion R. Applications and current challenges of proteomic approaches, focusing on two-dimensional electrophoresis. Amino Acids 2006; 33:405-14. [PMID: 17136510 DOI: 10.1007/s00726-006-0460-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2006] [Accepted: 10/10/2006] [Indexed: 01/23/2023]
Abstract
Since the formulation of the concept of "proteomics" in 1995, a plethora of proteomic technologies have been developed in order to study proteomes of tissues, cells and organelles. The powerful new technologies enabled by proteomic approaches have lead to the application of these methods to an exponentially increasing variety of biological questions for highly complex protein mixtures. Continuous technical optimization allows for an ever-increasing sensitivity of proteomic techniques. In this review, a brief overview of currently available proteomic techniques and their applications is given, followed by a more detailed description of advantages and technical challenges of two-dimensional electrophoresis (2-DE). Some solutions to circumvent currently encountered technical difficulties for 2-DE analyses are proposed.
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Affiliation(s)
- F G G Vercauteren
- Douglas Hospital Research Center, Department of Psychiatry, McGill University, Montréal, Québec, Canada
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